3/20/2019

Outline

  • Visualization for static network:
    • Graph: hairball plot
    • Matrix: heatmap in R basic package; geom_tile in pkg ggplot2
  • Other static networks:
    • Two-mode networks (node-specific attribute)
    • Multiple networks (edge-specific attribute)
    • … ( ggtree, ggalluvial, etc.)
  • ggplot2 version for network visualization:
    • Comparison between ggnet2,geomnet,ggnetwork
    • Extension to interactive (plotly) , dynamic network (ggnetwork)
  • Other interactive network visualizations:
    • visNetwork (good documentation)
    • networkD3
    • threejs
    • ggigraph
  • Visualization for dynamic networks
    • Snapshots for the evolving networks: ggnetwork (common)
    • Animation for the evolving networks: ggplot2 + gganimate
    • ndtv pkg (good documentation)

Available R packages and tutorial

ggplot2 version for network visualization

Comparison among the three R packages: https://journal.r-project.org/archive/2017/RJ-2017-023/RJ-2017-023.pdf

Interactive network visualization

Dynamic network

Tutorial:

Preparation

library(igraph)
library(igraphdata)
data(karate)

Other visualization for static network

Hairball plot

dia_vk=get_diameter(karate,directed = FALSE)
ecol=rep("gray80",ecount(karate))
ecol[E(karate,path = dia_vk)]="orange"
ew=rep(1,ecount(karate))
ew[E(karate,path = dia_vk)]=3
ls=list(`1`=which(V(karate)$Faction==1),`2`=which(V(karate)$Faction==2))
set.seed(1)
plot(karate,edge.color=ecol,edge.width=ew,mark.groups = ls)

#,vertex.size=log(degree(karate))*7+1

Heatmap

karate.mat=get.adjacency(karate,sparse = FALSE)
heatmap(karate.mat[,34:1],Rowv = NA, Colv = NA,scale="none")

# By default, Rowv and Colv will provide us the dendrogram
#scale=c("row","column","none") -- normalize the values
heatmap(karate.mat[,34:1])

?heatmap

Using geom_tile in R package ggplot2:

library(dplyr)
library(ggplot2)

# Change to long format. -- edgelist but including all the 0s 
longData=reshape2::melt(karate.mat)
  longData_all=as_tibble(longData)
  longData_all1=longData_all%>%mutate(Var1=forcats::fct_rev(Var1))

# using geom_tile
ggplot(longData_all1, aes(x = Var2, y = Var1)) + 
  geom_tile(aes(fill=value)) + 
  scale_fill_gradient(low="white", high="#333333",na.value = "red") + 
  theme_bw()+ggtitle("")+xlab("")+ylab("")+ #set clean background and no titles 
  guides(fill = guide_colourbar(barheight = 12))+ # can set the length of colour bar
  theme(axis.text.x = element_text(angle = 90, hjust = 1))+
  coord_fixed() # fix to square coordinator

Other static networks

Other static networks

- Two-mode networks (different shape, facets)
- Multiple networks (different color of edges, facets)
- `ggtree`
- `ggalluvial`

Two-mode network

  • graph_from_incidence_matrix: add a vertex attribute called “type”

  • can use different node-specific plotting parameter (shape,color,label) to indicate the type

  • has it own layout, layout_as_bipartite

set.seed(1)
twomode.mat=matrix(sample(c(0,1),9,replace = TRUE),nrow = 3)
rownames(twomode.mat)=c("A","B","C")
colnames(twomode.mat)=1:3
twomode.mat
##   1 2 3
## A 0 1 1
## B 0 0 1
## C 1 1 1
twomode.net=graph_from_incidence_matrix(twomode.mat)
plot(twomode.net)

vertex_attr_names(twomode.net)
## [1] "type" "name"
V(twomode.net)$type
## [1] FALSE FALSE FALSE  TRUE  TRUE  TRUE
V(twomode.net)$color <- c("blue", "orange")[V(twomode.net)$type+1]
V(twomode.net)$shape <- c("square", "circle")[V(twomode.net)$type+1]
plot(twomode.net,vertex.label.color="white")

plot(twomode.net,vertex.label.color="white",layout=layout_as_bipartite)

Multiple neworks

  • can use different edge-specific plotting parameters (color,linetype) to indicate the type
  • simplify the network by types.
  • can use different facet to present different networks with fixing layout (using ggnetwork will be more convenient)
data(enron)
subenron=induced_subgraph(enron,V(enron)[1:30])
subenron
## IGRAPH d238df7 D--- 30 2133 -- Enron email network
## + attr: LDC_names (g/c), LDC_desc (g/c), name (g/c), Citation
## | (g/c), Email (v/c), Name (v/c), Note (v/c), Time (e/c),
## | Reciptype (e/c), Topic (e/n), LDC_topic (e/n)
## + edges from d238df7:
##  [1] 1->10 1->10 1->10 1->10 1->10 1->10 1->10 1->10 1->10 1->10 1->10
## [12] 1->10 1->10 1->10 1->10 1->10 1->10 1->10 1->10 1->10 1->10 1->10
## [23] 1->10 1->21 1->21 1->21 1->21 2-> 2 2->16 2->16 2->16 2->16 2->16
## [34] 2->16 2->16 3->11 3->11 3->11 3->11 3->18 3->18 3->18 3->18 5-> 2
## [45] 5-> 2 5-> 2 5-> 2 5-> 2 5-> 2 5-> 5 5-> 5 5-> 5 5-> 5 5-> 5 5-> 5
## [56] 5-> 5 5-> 5 5-> 5 5-> 6 5-> 6 5-> 6 5-> 6 5-> 6 5-> 6 5-> 7 5-> 7
## + ... omitted several edges
E(subenron)$Reciptype%>%unique()
## [1] "to"  "bcc" "cc"
E(subenron)$color <- c("gold", "tomato", "yellowgreen")[E(subenron)$Reciptype%>%as.factor()]
set.seed(1)
plot(subenron,edge.arrow.size=0.2,layout=layout_in_circle,vertex.label=NA,vertex.size=2)

#merge the edges by type 
subenron.df=igraph::as_data_frame(subenron)
se.df=subenron.df%>%group_by(from,to,Reciptype)%>%summarise(weight=n())

se.net=graph_from_data_frame(se.df)
E(se.net)$color <- c("gold", "tomato", "yellowgreen")[E(se.net)$Reciptype%>%as.factor()]
set.seed(1)
plot(se.net,edge.arrow.size=0.2,layout=layout_in_circle,vertex.label=NA,vertex.size=2)

#edge.width=log(E(se.net)$weight+0.1)/4 #can set the width of edge

To delete edges, using - or delete_edges(graph,edges)

To keep the subgraph with specific edges, using subgraph.edges(graph, eids, delete.vertices = FALSE)

set.seed(1)
#fix the layout
l=layout_in_circle(se.net)
plot(se.net,edge.arrow.size=0.2,layout=l,vertex.shape="none")

#delete the edges
se.net.to=se.net-E(se.net)[E(se.net)$Reciptype%in%c("cc","bcc")]
#se.net.to=delete.edges(se.net,E(se.net)[E(se.net)$Reciptype%in%c("cc","bcc")]) #another way to delete
#se.net.to=subgraph.edges(se.net,E(se.net)[E(se.net)$Reciptype=="to"],delete.vertices = FALSE) # keep the subgraph 
se.net.cc=se.net-E(se.net)[E(se.net)$Reciptype%in%c("to","bcc")]
se.net.bcc=se.net-E(se.net)[E(se.net)$Reciptype%in%c("to","cc")]
par(mfrow=c(1,3))
plot(se.net.to,edge.arrow.size=0.2,layout=l,vertex.shape="none")
plot(se.net.cc,edge.arrow.size=0.2,layout=l,vertex.shape="none")
plot(se.net.bcc,edge.arrow.size=0.2,layout=l,vertex.shape="none")

ggplot2 version for network visualization

ggnet2,geomnet,ggnetwork

ggplot2 version for network visualization

Comparison among the three R packages: https://journal.r-project.org/archive/2017/RJ-2017-023/RJ-2017-023.pdf

All based on ggplot2 and network

  • ggnet2 has similar syntax as plot. easy to use.
  • geomnet add available layer geom_net in ggplot2. use dataframe as input. can interact with plotly
  • ggnetwork is most flexible. advantages on dynamic network.

football data

#install.packages("GGally")
library("GGally")
#install.packages("geomnet")
library("geomnet")
#install.packages("ggnetwork")
library("ggnetwork")
library("statnet")
# load the data
data("football",package = "geomnet")
rownames(football$vertices) <-football$vertices$label
# create network from edge list
fb.net=network::network(football$edges[,1:2])

# add vertex attribute: the conference the team is in
fb.net %v% "conf" <-football$vertices[network.vertex.names(fb.net), "value"]
# add edge attribute: whether two teams belong to the same conference
set.edge.attribute(fb.net, "same.conf",football$edges$same.conf)
set.edge.attribute(fb.net, "lty", ifelse(fb.net %e% "same.conf" == 1, 1, 2))

ggnet2

Features:

  • Input: network object
  • Available detailed tutorial. https://briatte.github.io/ggnet/
  • Syntax is similar to plot
  • Output the underlying organized struture (positions of nodes). Easy to add geom_xx

Issues:

  • No curved edges
  • No self-loops
  • No complex graphs
  • For evolving graphs, cannot provide multiple facet directly. Need to fix the placement coordinates.
ggnet2(fb.net, mode = "fruchtermanreingold",
color = "conf", palette = "Paired",
color.legend = "Conference",
edge.color = c("color", "grey75"))

set.seed(3212019)
pggnet2=
  ggnet2(fb.net, # input `network` object
       mode = "fruchtermanreingold", # layout from `network` pkg
       layout.par = list(cell.jitter=0.75), #can pass the layout args 
       #node attribute
       node.color = "conf", 
       palette = "Paired", #palette="Set3",
       node.size=5,
       #node.size="degree",
       #size.cut=3, # cut the size to three categories using quantiles
       #size="conf", 
       #to manual mapping the size: size.palette=c("Atlantic Coast"=1,...),
       #node.shape = "conf",
       node.alpha = 0.5,
       #node.label = TRUE,
       #edge
       edge.color = c("color", "grey50"), #1st value: same col as node for same group. else 2nd args.
       edge.alpha = 0.5,
       edge.size=0.3,
       edge.lty = "lty",
       #edge.label = 1,
       #edge.label.size=1,
       #legend
       color.legend = "Conference",
       #legend.size = 10, 
       #legend.position = "bottom")
)+ 
  geom_point(aes(color = color), size = 3) # can be treat as ggplot object and add geom_xx layer
pggnet2

## treat it as dataframe to add geom_xx layer
pggnet2$data%>%names()
## [1] "label" "alpha" "color" "shape" "size"  "x"     "y"

geomnet

Features:

  • Input: dataframe
  • Allow self-loops
  • Allow facet (cannot fix the nodes)

Issues:

  • No available detailed tutorial.
  • The underlying structured is not available. It is wrapped as a whole. (eg. if setting alpha, is for both nodes and edges; do not provide the positions of points)
  • Obey the ggplot2 syntax “strictly”, less flexible
#merge the vertex and edges
ver.conf=football$vertices%>%mutate(from=label)%>%select(-label)
fb.df=left_join(football$edges,ver.conf,by="from")
# create data plot
set.seed(3212019)
pgeomnet=
  ggplot(data = fb.df, # input: dataframe
  aes(from_id = from, to_id = to)) +
  geom_net(layout.alg = 'fruchtermanreingold',
  aes(colour = value, group = value,
  linetype = factor(same.conf != 1)),
  linewidth = 0.5,
  size = 5, vjust = -0.75, alpha = 1) +
  theme_net() +
  #theme(legend.position = "bottom") +
  scale_colour_brewer("Conference", palette = "Paired") +
  guides(linetype = FALSE)
pgeomnet

## the underlying dataframe is not point + line
pgeomnet$data%>%names()
## [1] "from"      "to"        "same.conf" "value"

ggnetwork

Features:

  • Available detailed tutorial, https://briatte.github.io/ggnetwork/
  • Input: igraph(need library(intergraph)) or network object
  • Syntax is super userfriendly.
    • ggnetwork provide the underlying dataframe
    • use geom_edges and geom_nodes separately; can set edge/node-specific mapping within the geom_xx
    • for labels geom_(node/edge)(text/label)[_repel]: geom_nodetext, geom_nodelabel, geom_nodetext_repel, geom_nodelabel_repel,geom_edgetext, geom_edgelabel, geom_edgetext_repel, geom_edgelabel_repel
  • Allow curve edges (but is compatible with plotly)
  • Can represent dynamic networks using facet with fixing the positions of node

Issues:

  • No self-loops
## igraph object
fb.igra=graph_from_data_frame(football$edges[,1:2],directed = FALSE)
V(fb.igra)$conf=football$vertices[V(fb.igra)$name, "value"]
E(fb.igra)$same.conf=football$edges$same.conf
E(fb.igra)$lty=ifelse(E(fb.igra)$same.conf == 1, 1, 2)
#need to load this for igraph object
#install.packages("intergraph")
library("intergraph")
#Tips: ctrl+shift+A to reformat
set.seed(3212019)
pggnetwork=
  ggplot(
  ggnetwork(# provide the underlying dataframe
    fb.igra, #input: network object
    layout = "fruchtermanreingold",  #layout
    cell.jitter = 0.75),
  #can pass layout parameter
  aes(x, y, xend = xend, yend = yend)
) + #mapping for edges
  geom_edges(aes(linetype = as.factor(same.conf)),
             #arrow = arrow(length = unit(6, "pt"), type = "closed") #if directed
             color = "grey50",
             curvature = 0.2,
             alpha=0.5
             ) +
  geom_nodes(aes(color = conf), 
             size = 5,
             alpha=0.5) +
  scale_color_brewer("Conference",
                     palette = "Paired") +
  scale_linetype_manual(values = c(2, 1)) +
  guides(linetype = FALSE) +
  theme_blank()+ 
  geom_nodes(aes(color = conf), 
             size = 3) # can be treat as ggplot object and add geom_xx layer
pggnetwork

## treat it as dataframe to add geom_xx layer
pggnetwork$data%>%names()
##  [1] "x"            "y"            "conf"         "na.x"        
##  [5] "vertex.names" "xend"         "yend"         "lty"         
##  [9] "na.y"         "same.conf"

Extensions of ggnet2,geomnet,ggnetwork

Since the output is ggplot2 object,

  • Interactive network visualization: ggplot2 + plotly

  • Dynamic network: facet ggnetwork

ggplot2 + plotly

library("plotly")
ggplotly(pggnet2+coord_fixed())%>%hide_guides()
ggplotly(pgeomnet+coord_fixed())%>%hide_guides()
## Joining, by = c("colour", "linetype", "from", "to", "x", "y", "xend", "yend", "group", "PANEL", ".selfie", "weight", ".samegroup", "ymax", "xmax", "width", "fontsize", "shape", "arrowsize", "size", "fill", "alpha", "stroke", "linewidth", "angle", "vjust", "hjust", "curvature")
## Warning: Aspect ratios aren't yet implemented, but you can manually set a
## suitable height/width

## Warning: Aspect ratios aren't yet implemented, but you can manually set a
## suitable height/width
#if set the `curvature` of the edge, the plotly will not show.
#ggplotly(pggnetwork+coord_fixed())%>%hide_guides()
pggnetwork2=
  ggplot(
  ggnetwork(# provide the underlying dataframe
    fb.igra, #input: network object
    layout = "fruchtermanreingold",  #layout
    cell.jitter = 0.75),
  #can pass layout parameter
  aes(x, y, xend = xend, yend = yend)
) + #mapping for edges
  geom_edges(aes(linetype = as.factor(same.conf)),
             #arrow = arrow(length = unit(6, "pt"), type = "closed") #if directed
             color = "grey50",
             #curvature = 0.2,
             alpha=0.5
             ) +
  geom_nodes(aes(color = conf), 
             size = 5,
             alpha=0.5) +
  scale_color_brewer("Conference",
                     palette = "Paired") +
  scale_linetype_manual(values = c(2, 1)) +
  guides(linetype = FALSE) +
  theme_blank()+ 
  geom_nodes(aes(color = conf), 
             size = 3) 
ggplotly(pggnetwork2+coord_fixed())%>%hide_guides()

Facet dynamic network

Recommend using ggnetwork

## create network
names(email$edges)
## [1] "From"        "eID"         "Date"        "Subject"     "to"         
## [6] "month"       "day"         "year"        "nrecipients"
names(email$nodes)
##  [1] "label"                      "LastName"                  
##  [3] "FirstName"                  "BirthDate"                 
##  [5] "BirthCountry"               "Gender"                    
##  [7] "CitizenshipCountry"         "CitizenshipBasis"          
##  [9] "CitizenshipStartDate"       "PassportCountry"           
## [11] "PassportIssueDate"          "PassportExpirationDate"    
## [13] "CurrentEmploymentType"      "CurrentEmploymentTitle"    
## [15] "CurrentEmploymentStartDate" "MilitaryServiceBranch"     
## [17] "MilitaryDischargeType"      "MilitaryDischargeDate"
#edgelist: remove emails sent to all employees
edges=email$edges%>%filter(nrecipients < 54)%>%select(From,to,day)
# Create network 
em.net <- network(edges[, 1:2])
# assign edge attributes (day)
set.edge.attribute(em.net, "day", edges[, 3])
# assign vertex attributes (employee type)
em.cet <- as.character(email$nodes$CurrentEmploymentType)
names(em.cet) = email$nodes$label
em.net %v% "curr_empl_type" <- em.cet[ network.vertex.names(em.net) ]
set.seed(3212019)
ggplot(
  ggnetwork(
    em.net,
    arrow.gap = 0.02,
    by = "day",
    layout = "kamadakawai"
  ),
  aes(x, y, xend = xend, yend = yend)
) +
  geom_edges(
    aes(color = curr_empl_type),
    alpha = 0.25,
    arrow = arrow(length = unit(5, "pt"), type = "closed")
  ) +
  geom_nodes(aes(color = curr_empl_type), size = 1.5) +
  scale_color_brewer("Employment Type", palette = "Set1") +
  facet_wrap( .~ day, nrow = 2, labeller = "label_both") +
  theme_facet(legend.position = "bottom")
## Warning in fortify.network(x, ...): duplicated edges detected

Comments

The main part of network visualization is the layout of the nodes.All the mentioned R pkg automatically generate the positions of points in the layer. If you want to build a network with pre-specified locations for each node, just draw the points and lines using plot or ggplot.

See Chapter 8 Overlaying networks on geographic in http://kateto.net/network-visualization

Interactive network visualization

Dynamic network

Reference